Plot Data
library(ggplot2)
# raw data
ggplot(dataset, aes(x=Olaparib, y=Counts)) +
theme_bw() +
theme(panel.grid=element_blank(), text = element_text(size=14)) +
geom_smooth(method=lm, formula = y ~ poly(x,2), se=FALSE, aes(colour=siRNA)) +
geom_point(aes(colour=siRNA, shape=Experiment), size=2) +
facet_grid(. ~ genotype) +
xlab(label = "Olaparib (log10 nM)") +
scale_shape_manual(values=15:19) +
scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

# NormCounts Linear
ggplot(dataset, aes(x=Olaparib, y=NormCounts, color=siRNA)) +
theme_bw() +
theme(panel.grid=element_blank(), text = element_text(size=14)) +
geom_point(aes(colour=siRNA), size=2) +
geom_smooth(method=lm, formula = y ~ x, se=FALSE) +
facet_grid(. ~ genotype) +
xlab(label = "Olaparib (log10 nM)") +
scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

# NormCounts2 Linear
ggplot(dataset, aes(x=Olaparib, y=NormCounts2, color=siRNA)) +
theme_bw() +
theme(panel.grid=element_blank(), text = element_text(size=14)) +
geom_point(aes(colour=siRNA), size=2) +
geom_smooth(method=lm, formula = y ~ x, se=FALSE) +
facet_grid(. ~ genotype) +
xlab(label = "Olaparib (log10 nM)") +
scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

# NormCounts Quadratic
ggplot(dataset, aes(x=Olaparib, y=NormCounts, color=siRNA)) +
theme_bw() +
theme(panel.grid=element_blank(), text = element_text(size=14)) +
geom_point(aes(colour=siRNA), size=2) +
geom_smooth(method=lm, formula = y ~ poly(x,2), se=FALSE) +
facet_grid(. ~ genotype) +
xlab(label = "Olaparib (log10 nM)")+
scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

# NormCounts2 Quadratic
ggplot(dataset, aes(x=Olaparib, y=NormCounts2, color=siRNA)) +
theme_bw() +
theme(panel.grid=element_blank(), text = element_text(size=14)) +
geom_point(aes(colour=siRNA), size=2) +
geom_smooth(method=lm, formula = y ~ poly(x,2), se=FALSE) +
facet_grid(. ~ genotype) +
xlab(label = "Olaparib (log10 nM)") +
scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

# NormCounts Cubic
ggplot(dataset, aes(x=Olaparib, y=NormCounts, color=siRNA)) +
theme_bw() +
theme(panel.grid=element_blank(), text = element_text(size=14)) +
geom_point(aes(colour=siRNA), size=2) +
geom_smooth(method=lm, formula = y ~ poly(x,3), se=FALSE) +
facet_grid(. ~ genotype) +
xlab(label = "Olaparib (log10 nM)")+
scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

# NormCounts2 Cubic
ggplot(dataset, aes(x=Olaparib, y=NormCounts2, color=siRNA)) +
theme_bw() +
theme(panel.grid=element_blank(), text = element_text(size=14)) +
geom_point(aes(colour=siRNA), size=2) +
geom_smooth(method=lm, formula = y ~ poly(x,3), se=FALSE) +
facet_grid(. ~ genotype) +
xlab(label = "Olaparib (log10 nM)") +
scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

library(Cairo)
cairo_pdf("FigureS5A.pdf", width = 8, height = 4, family = "Arial")
ggplot(dataset, aes(x=Olaparib, y=NormCounts2)) +
theme_bw() +
theme(panel.grid=element_blank(), text = element_text(size=14)) +
geom_point(aes(colour = siRNA)) +
geom_smooth(method=lm, formula = y ~ poly(x,2), se=TRUE, aes(colour = siRNA), fill='#DDDDDD', size=0.5) +
facet_grid(. ~ genotype) +
xlab(label = "Olaparib (log10 nM)") +
ylab(label = "Normalized Counts") +
scale_color_manual(values=c("#000000","#008000","#808080","#008080"))
dev.off()
## quartz_off_screen
## 2
Models
library(MASS)
library(DHARMa)
library(lme4)
library(lmerTest)
library(bbmle)
Linear formula
fit1 <- lm(Counts ~ Experiment + Olaparib*siRNA*genotype, data = dataset)
print(summary(fit1))
##
## Call:
## lm(formula = Counts ~ Experiment + Olaparib * siRNA * genotype,
## data = dataset)
##
## Residuals:
## Min 1Q Median 3Q Max
## -713.14 -258.88 18.63 224.08 920.16
##
## Coefficients:
## Estimate Std. Error t value
## (Intercept) 2486.513 167.388 14.855
## Experimentexp2 445.938 89.908 4.960
## Experimentexp3 389.250 89.908 4.329
## Experimentexp4 -197.375 89.908 -2.195
## Olaparib -279.540 69.982 -3.994
## siRNAsi53BP1 80.926 223.550 0.362
## siRNAsi53BP1+siBRCA1 -662.557 223.550 -2.964
## siRNAsiBRCA1 -1211.136 223.550 -5.418
## genotypeALC1KO -938.475 223.550 -4.198
## Olaparib:siRNAsi53BP1 -64.955 98.969 -0.656
## Olaparib:siRNAsi53BP1+siBRCA1 84.874 98.969 0.858
## Olaparib:siRNAsiBRCA1 13.698 98.969 0.138
## Olaparib:genotypeALC1KO -149.784 98.969 -1.513
## siRNAsi53BP1:genotypeALC1KO -558.350 316.148 -1.766
## siRNAsi53BP1+siBRCA1:genotypeALC1KO -192.261 316.148 -0.608
## siRNAsiBRCA1:genotypeALC1KO 5.367 316.148 0.017
## Olaparib:siRNAsi53BP1:genotypeALC1KO 202.473 139.964 1.447
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO 119.029 139.964 0.850
## Olaparib:siRNAsiBRCA1:genotypeALC1KO 276.501 139.964 1.976
## Pr(>|t|)
## (Intercept) < 2e-16 ***
## Experimentexp2 2.61e-06 ***
## Experimentexp3 3.33e-05 ***
## Experimentexp4 0.030262 *
## Olaparib 0.000118 ***
## siRNAsi53BP1 0.718051
## siRNAsi53BP1+siBRCA1 0.003732 **
## siRNAsiBRCA1 3.64e-07 ***
## genotypeALC1KO 5.52e-05 ***
## Olaparib:siRNAsi53BP1 0.513007
## Olaparib:siRNAsi53BP1+siBRCA1 0.393008
## Olaparib:siRNAsiBRCA1 0.890178
## Olaparib:genotypeALC1KO 0.133063
## siRNAsi53BP1:genotypeALC1KO 0.080178 .
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.544362
## siRNAsiBRCA1:genotypeALC1KO 0.986486
## Olaparib:siRNAsi53BP1:genotypeALC1KO 0.150876
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.396954
## Olaparib:siRNAsiBRCA1:genotypeALC1KO 0.050737 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 359.6 on 109 degrees of freedom
## Multiple R-squared: 0.8584, Adjusted R-squared: 0.835
## F-statistic: 36.71 on 18 and 109 DF, p-value: < 2.2e-16
cat("AIC: ", AIC(fit1))
## AIC: 1889.261
simres <- simulateResiduals(fittedModel = fit1)
plot(simres)

fit2 <- lm(NormCounts ~ Olaparib*siRNA*genotype, data = dataset)
print(summary(fit2))
##
## Call:
## lm(formula = NormCounts ~ Olaparib * siRNA * genotype, data = dataset)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.5166 -0.1169 0.0066 0.1040 0.7429
##
## Coefficients:
## Estimate Std. Error t value
## (Intercept) 1.25213 0.08809 14.215
## Olaparib -0.13571 0.03900 -3.480
## siRNAsi53BP1 0.07162 0.12457 0.575
## siRNAsi53BP1+siBRCA1 0.01937 0.12457 0.155
## siRNAsiBRCA1 0.29335 0.12457 2.355
## genotypeALC1KO 0.65514 0.12457 5.259
## Olaparib:siRNAsi53BP1 -0.03855 0.05515 -0.699
## Olaparib:siRNAsi53BP1+siBRCA1 -0.01043 0.05515 -0.189
## Olaparib:siRNAsiBRCA1 -0.15790 0.05515 -2.863
## Olaparib:genotypeALC1KO -0.35263 0.05515 -6.394
## siRNAsi53BP1:genotypeALC1KO -0.14870 0.17617 -0.844
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.13138 0.17617 0.746
## siRNAsiBRCA1:genotypeALC1KO -0.15105 0.17617 -0.857
## Olaparib:siRNAsi53BP1:genotypeALC1KO 0.08004 0.07799 1.026
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.07072 0.07799 -0.907
## Olaparib:siRNAsiBRCA1:genotypeALC1KO 0.08131 0.07799 1.042
## Pr(>|t|)
## (Intercept) < 2e-16 ***
## Olaparib 0.000715 ***
## siRNAsi53BP1 0.566486
## siRNAsi53BP1+siBRCA1 0.876710
## siRNAsiBRCA1 0.020270 *
## genotypeALC1KO 7.02e-07 ***
## Olaparib:siRNAsi53BP1 0.485991
## Olaparib:siRNAsi53BP1+siBRCA1 0.850393
## Olaparib:siRNAsiBRCA1 0.005009 **
## Olaparib:genotypeALC1KO 3.84e-09 ***
## siRNAsi53BP1:genotypeALC1KO 0.400415
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.457374
## siRNAsiBRCA1:genotypeALC1KO 0.393037
## Olaparib:siRNAsi53BP1:genotypeALC1KO 0.306980
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.366510
## Olaparib:siRNAsiBRCA1:genotypeALC1KO 0.299436
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.2004 on 112 degrees of freedom
## Multiple R-squared: 0.8791, Adjusted R-squared: 0.8629
## F-statistic: 54.27 on 15 and 112 DF, p-value: < 2.2e-16
cat("AIC: ", AIC(fit2))
## AIC: -31.34769
simres <- simulateResiduals(fittedModel = fit2)
plot(simres)

fit3 <- lm(NormCounts2 ~ Olaparib*siRNA*genotype, data = dataset)
print(summary(fit3))
##
## Call:
## lm(formula = NormCounts2 ~ Olaparib * siRNA * genotype, data = dataset)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.23675 -0.06789 0.00460 0.06796 0.32683
##
## Coefficients:
## Estimate Std. Error t value
## (Intercept) 1.053158 0.047016 22.400
## Olaparib -0.114146 0.020815 -5.484
## siRNAsi53BP1 -0.007063 0.066491 -0.106
## siRNAsi53BP1+siBRCA1 -0.048008 0.066491 -0.722
## siRNAsiBRCA1 -0.060219 0.066491 -0.906
## genotypeALC1KO -0.130076 0.066491 -1.956
## Olaparib:siRNAsi53BP1 -0.023565 0.029437 -0.801
## Olaparib:siRNAsi53BP1+siBRCA1 -0.001379 0.029437 -0.047
## Olaparib:siRNAsiBRCA1 -0.074492 0.029437 -2.531
## Olaparib:genotypeALC1KO -0.122204 0.029437 -4.151
## siRNAsi53BP1:genotypeALC1KO 0.047067 0.094032 0.501
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.030343 0.094032 0.323
## siRNAsiBRCA1:genotypeALC1KO 0.103308 0.094032 1.099
## Olaparib:siRNAsi53BP1:genotypeALC1KO 0.024770 0.041630 0.595
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.012815 0.041630 -0.308
## Olaparib:siRNAsiBRCA1:genotypeALC1KO 0.044529 0.041630 1.070
## Pr(>|t|)
## (Intercept) < 2e-16 ***
## Olaparib 2.61e-07 ***
## siRNAsi53BP1 0.9156
## siRNAsi53BP1+siBRCA1 0.4718
## siRNAsiBRCA1 0.3671
## genotypeALC1KO 0.0529 .
## Olaparib:siRNAsi53BP1 0.4251
## Olaparib:siRNAsi53BP1+siBRCA1 0.9627
## Olaparib:siRNAsiBRCA1 0.0128 *
## Olaparib:genotypeALC1KO 6.47e-05 ***
## siRNAsi53BP1:genotypeALC1KO 0.6177
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.7475
## siRNAsiBRCA1:genotypeALC1KO 0.2743
## Olaparib:siRNAsi53BP1:genotypeALC1KO 0.5530
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.7588
## Olaparib:siRNAsiBRCA1:genotypeALC1KO 0.2871
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.107 on 112 degrees of freedom
## Multiple R-squared: 0.9007, Adjusted R-squared: 0.8875
## F-statistic: 67.76 on 15 and 112 DF, p-value: < 2.2e-16
cat("AIC: ", AIC(fit3))
## AIC: -192.0674
simres <- simulateResiduals(fittedModel = fit3)
plot(simres)

fit4 <- lmer(Counts ~ Olaparib*siRNA*genotype + (1|UID), data = dataset)
print(summary(fit4))
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Counts ~ Olaparib * siRNA * genotype + (1 | UID)
## Data: dataset
##
## REML criterion at convergence: 1622.4
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.9007 -0.5748 -0.0717 0.5734 2.2507
##
## Random effects:
## Groups Name Variance Std.Dev.
## UID (Intercept) 197856 444.8
## Residual 38460 196.1
## Number of obs: 128, groups: UID, 32
##
## Fixed effects:
## Estimate Std. Error df
## (Intercept) 2645.966 238.525 28.803
## Olaparib -279.540 38.162 88.000
## siRNAsi53BP1 80.926 337.326 28.803
## siRNAsi53BP1+siBRCA1 -662.557 337.326 28.803
## siRNAsiBRCA1 -1211.136 337.326 28.803
## genotypeALC1KO -938.475 337.326 28.803
## Olaparib:siRNAsi53BP1 -64.955 53.969 88.000
## Olaparib:siRNAsi53BP1+siBRCA1 84.874 53.969 88.000
## Olaparib:siRNAsiBRCA1 13.698 53.969 88.000
## Olaparib:genotypeALC1KO -149.784 53.969 88.000
## siRNAsi53BP1:genotypeALC1KO -558.350 477.051 28.803
## siRNAsi53BP1+siBRCA1:genotypeALC1KO -192.261 477.051 28.803
## siRNAsiBRCA1:genotypeALC1KO 5.367 477.051 28.803
## Olaparib:siRNAsi53BP1:genotypeALC1KO 202.473 76.324 88.000
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO 119.029 76.324 88.000
## Olaparib:siRNAsiBRCA1:genotypeALC1KO 276.501 76.324 88.000
## t value Pr(>|t|)
## (Intercept) 11.093 6.50e-12 ***
## Olaparib -7.325 1.08e-10 ***
## siRNAsi53BP1 0.240 0.812104
## siRNAsi53BP1+siBRCA1 -1.964 0.059229 .
## siRNAsiBRCA1 -3.590 0.001209 **
## genotypeALC1KO -2.782 0.009428 **
## Olaparib:siRNAsi53BP1 -1.204 0.231992
## Olaparib:siRNAsi53BP1+siBRCA1 1.573 0.119393
## Olaparib:siRNAsiBRCA1 0.254 0.800239
## Olaparib:genotypeALC1KO -2.775 0.006735 **
## siRNAsi53BP1:genotypeALC1KO -1.170 0.251425
## siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.403 0.689909
## siRNAsiBRCA1:genotypeALC1KO 0.011 0.991101
## Olaparib:siRNAsi53BP1:genotypeALC1KO 2.653 0.009470 **
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO 1.560 0.122465
## Olaparib:siRNAsiBRCA1:genotypeALC1KO 3.623 0.000487 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
cat("AIC: ", AIC(fit4))
## AIC: 1658.358
simres <- simulateResiduals(fittedModel = fit4)
plot(simres)

Quadratic formula
fit5 <- lm(Counts ~ Experiment + poly(Olaparib,2)*siRNA*genotype, data = dataset)
print(summary(fit5))
##
## Call:
## lm(formula = Counts ~ Experiment + poly(Olaparib, 2) * siRNA *
## genotype, data = dataset)
##
## Residuals:
## Min 1Q Median 3Q Max
## -653.69 -238.10 9.73 216.34 849.41
##
## Coefficients:
## Estimate Std. Error
## (Intercept) 1967.17 104.62
## Experimentexp2 445.94 89.22
## Experimentexp3 389.25 89.22
## Experimentexp4 -197.37 89.22
## poly(Olaparib, 2)1 -4063.13 1009.39
## poly(Olaparib, 2)2 -1834.91 1009.39
## siRNAsi53BP1 -39.75 126.17
## siRNAsi53BP1+siBRCA1 -504.87 126.17
## siRNAsiBRCA1 -1185.69 126.17
## genotypeALC1KO -1216.75 126.17
## poly(Olaparib, 2)1:siRNAsi53BP1 -944.12 1427.49
## poly(Olaparib, 2)2:siRNAsi53BP1 302.40 1427.49
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1 1233.64 1427.49
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1 1565.84 1427.49
## poly(Olaparib, 2)1:siRNAsiBRCA1 199.10 1427.49
## poly(Olaparib, 2)2:siRNAsiBRCA1 2351.59 1427.49
## poly(Olaparib, 2)1:genotypeALC1KO -2177.12 1427.49
## poly(Olaparib, 2)2:genotypeALC1KO 3444.07 1427.49
## siRNAsi53BP1:genotypeALC1KO -182.19 178.44
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 28.87 178.44
## siRNAsiBRCA1:genotypeALC1KO 519.06 178.44
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO 2942.95 2018.78
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO -1295.71 2018.78
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO 1730.08 2018.78
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -2295.16 2018.78
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO 4018.95 2018.78
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO -3685.15 2018.78
## t value Pr(>|t|)
## (Intercept) 18.803 < 2e-16 ***
## Experimentexp2 4.998 2.44e-06 ***
## Experimentexp3 4.363 3.10e-05 ***
## Experimentexp4 -2.212 0.02920 *
## poly(Olaparib, 2)1 -4.025 0.00011 ***
## poly(Olaparib, 2)2 -1.818 0.07205 .
## siRNAsi53BP1 -0.315 0.75338
## siRNAsi53BP1+siBRCA1 -4.001 0.00012 ***
## siRNAsiBRCA1 -9.397 1.91e-15 ***
## genotypeALC1KO -9.643 5.48e-16 ***
## poly(Olaparib, 2)1:siRNAsi53BP1 -0.661 0.50987
## poly(Olaparib, 2)2:siRNAsi53BP1 0.212 0.83266
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1 0.864 0.38952
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1 1.097 0.27529
## poly(Olaparib, 2)1:siRNAsiBRCA1 0.139 0.88936
## poly(Olaparib, 2)2:siRNAsiBRCA1 1.647 0.10259
## poly(Olaparib, 2)1:genotypeALC1KO -1.525 0.13035
## poly(Olaparib, 2)2:genotypeALC1KO 2.413 0.01764 *
## siRNAsi53BP1:genotypeALC1KO -1.021 0.30968
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.162 0.87177
## siRNAsiBRCA1:genotypeALC1KO 2.909 0.00446 **
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO 1.458 0.14800
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO -0.642 0.52244
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.857 0.39348
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1.137 0.25827
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO 1.991 0.04921 *
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO -1.825 0.07089 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 356.9 on 101 degrees of freedom
## Multiple R-squared: 0.8708, Adjusted R-squared: 0.8375
## F-statistic: 26.18 on 26 and 101 DF, p-value: < 2.2e-16
cat("AIC: ", AIC(fit5))
## AIC: 1893.534
simres <- simulateResiduals(fittedModel = fit5)
plot(simres)

fit6 <- lm(NormCounts ~ poly(Olaparib,2)*siRNA*genotype, data = dataset)
print(summary(fit6))
##
## Call:
## lm(formula = NormCounts ~ poly(Olaparib, 2) * siRNA * genotype,
## data = dataset)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.49865 -0.08137 0.00024 0.08742 0.54005
##
## Coefficients:
## Estimate Std. Error
## (Intercept) 1.000e+00 4.146e-02
## poly(Olaparib, 2)1 -1.973e+00 4.691e-01
## poly(Olaparib, 2)2 -8.808e-01 4.691e-01
## siRNAsi53BP1 -2.231e-16 5.864e-02
## siRNAsi53BP1+siBRCA1 1.601e-16 5.864e-02
## siRNAsiBRCA1 2.393e-17 5.864e-02
## genotypeALC1KO -6.681e-16 5.864e-02
## poly(Olaparib, 2)1:siRNAsi53BP1 -5.603e-01 6.634e-01
## poly(Olaparib, 2)2:siRNAsi53BP1 1.255e-01 6.634e-01
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1 -1.515e-01 6.634e-01
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1 8.736e-01 6.634e-01
## poly(Olaparib, 2)1:siRNAsiBRCA1 -2.295e+00 6.634e-01
## poly(Olaparib, 2)2:siRNAsiBRCA1 1.021e+00 6.634e-01
## poly(Olaparib, 2)1:genotypeALC1KO -5.126e+00 6.634e-01
## poly(Olaparib, 2)2:genotypeALC1KO 2.709e+00 6.634e-01
## siRNAsi53BP1:genotypeALC1KO 1.460e-16 8.292e-02
## siRNAsi53BP1+siBRCA1:genotypeALC1KO -2.043e-16 8.292e-02
## siRNAsiBRCA1:genotypeALC1KO -4.197e-17 8.292e-02
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO 1.163e+00 9.382e-01
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO -1.002e+00 9.382e-01
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1.028e+00 9.382e-01
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1.787e-01 9.382e-01
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO 1.182e+00 9.382e-01
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO -1.788e+00 9.382e-01
## t value Pr(>|t|)
## (Intercept) 24.119 < 2e-16 ***
## poly(Olaparib, 2)1 -4.205 5.54e-05 ***
## poly(Olaparib, 2)2 -1.878 0.063219 .
## siRNAsi53BP1 0.000 1.000000
## siRNAsi53BP1+siBRCA1 0.000 1.000000
## siRNAsiBRCA1 0.000 1.000000
## genotypeALC1KO 0.000 1.000000
## poly(Olaparib, 2)1:siRNAsi53BP1 -0.845 0.400241
## poly(Olaparib, 2)2:siRNAsi53BP1 0.189 0.850307
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1 -0.228 0.819750
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1 1.317 0.190765
## poly(Olaparib, 2)1:siRNAsiBRCA1 -3.460 0.000786 ***
## poly(Olaparib, 2)2:siRNAsiBRCA1 1.539 0.126825
## poly(Olaparib, 2)1:genotypeALC1KO -7.726 7.25e-12 ***
## poly(Olaparib, 2)2:genotypeALC1KO 4.083 8.75e-05 ***
## siRNAsi53BP1:genotypeALC1KO 0.000 1.000000
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.000 1.000000
## siRNAsiBRCA1:genotypeALC1KO 0.000 1.000000
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO 1.240 0.217734
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO -1.068 0.288079
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1.096 0.275776
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.191 0.849282
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO 1.260 0.210604
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO -1.906 0.059369 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.1658 on 104 degrees of freedom
## Multiple R-squared: 0.9231, Adjusted R-squared: 0.9061
## F-statistic: 54.27 on 23 and 104 DF, p-value: < 2.2e-16
cat("AIC: ", AIC(fit6))
## AIC: -73.28383
simres <- simulateResiduals(fittedModel = fit6)
plot(simres)

fit7 <- lm(NormCounts2 ~ poly(Olaparib,2)*siRNA*genotype, data = dataset)
print(summary(fit7))
##
## Call:
## lm(formula = NormCounts2 ~ poly(Olaparib, 2) * siRNA * genotype,
## data = dataset)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.235066 -0.048533 0.000176 0.053866 0.242777
##
## Coefficients:
## Estimate Std. Error
## (Intercept) 0.841093 0.022641
## poly(Olaparib, 2)1 -1.659109 0.256151
## poly(Olaparib, 2)2 -0.740846 0.256151
## siRNAsi53BP1 -0.050843 0.032019
## siRNAsi53BP1+siBRCA1 -0.050571 0.032019
## siRNAsiBRCA1 -0.198613 0.032019
## genotypeALC1KO -0.357112 0.032019
## poly(Olaparib, 2)1:siRNAsi53BP1 -0.342512 0.362252
## poly(Olaparib, 2)2:siRNAsi53BP1 0.143967 0.362252
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1 -0.020047 0.362252
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1 0.735155 0.362252
## poly(Olaparib, 2)1:siRNAsiBRCA1 -1.082742 0.362252
## poly(Olaparib, 2)2:siRNAsiBRCA1 0.830908 0.362252
## poly(Olaparib, 2)1:genotypeALC1KO -1.776242 0.362252
## poly(Olaparib, 2)2:genotypeALC1KO 1.625433 0.362252
## siRNAsi53BP1:genotypeALC1KO 0.093085 0.045281
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.006535 0.045281
## siRNAsiBRCA1:genotypeALC1KO 0.186036 0.045281
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO 0.360026 0.512301
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO -0.527875 0.512301
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.186264 0.512301
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.509928 0.512301
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO 0.647226 0.512301
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO -1.215675 0.512301
## t value Pr(>|t|)
## (Intercept) 37.150 < 2e-16 ***
## poly(Olaparib, 2)1 -6.477 3.16e-09 ***
## poly(Olaparib, 2)2 -2.892 0.00466 **
## siRNAsi53BP1 -1.588 0.11534
## siRNAsi53BP1+siBRCA1 -1.579 0.11728
## siRNAsiBRCA1 -6.203 1.14e-08 ***
## genotypeALC1KO -11.153 < 2e-16 ***
## poly(Olaparib, 2)1:siRNAsi53BP1 -0.946 0.34659
## poly(Olaparib, 2)2:siRNAsi53BP1 0.397 0.69187
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1 -0.055 0.95597
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1 2.029 0.04497 *
## poly(Olaparib, 2)1:siRNAsiBRCA1 -2.989 0.00349 **
## poly(Olaparib, 2)2:siRNAsiBRCA1 2.294 0.02382 *
## poly(Olaparib, 2)1:genotypeALC1KO -4.903 3.49e-06 ***
## poly(Olaparib, 2)2:genotypeALC1KO 4.487 1.87e-05 ***
## siRNAsi53BP1:genotypeALC1KO 2.056 0.04232 *
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.144 0.88553
## siRNAsiBRCA1:genotypeALC1KO 4.108 7.96e-05 ***
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO 0.703 0.48377
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO -1.030 0.30521
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.364 0.71691
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.995 0.32187
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO 1.263 0.20928
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO -2.373 0.01948 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.09056 on 104 degrees of freedom
## Multiple R-squared: 0.9339, Adjusted R-squared: 0.9193
## F-statistic: 63.92 on 23 and 104 DF, p-value: < 2.2e-16
cat("AIC: ", AIC(fit7))
## AIC: -228.1676
simres <- simulateResiduals(fittedModel = fit7)
plot(simres)

fit8 <- lmer(Counts ~ poly(Olaparib,2)*siRNA*genotype + (1|UID), data = dataset)
print(summary(fit8))
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Counts ~ poly(Olaparib, 2) * siRNA * genotype + (1 | UID)
## Data: dataset
##
## REML criterion at convergence: 1427.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.52515 -0.47579 -0.02532 0.47074 2.39428
##
## Random effects:
## Groups Name Variance Std.Dev.
## UID (Intercept) 200751 448.1
## Residual 26878 163.9
## Number of obs: 128, groups: UID, 32
##
## Fixed effects:
## Estimate Std. Error
## (Intercept) 2126.62 227.74
## poly(Olaparib, 2)1 -4063.13 463.71
## poly(Olaparib, 2)2 -1834.91 463.71
## siRNAsi53BP1 -39.75 322.08
## siRNAsi53BP1+siBRCA1 -504.87 322.08
## siRNAsiBRCA1 -1185.69 322.08
## genotypeALC1KO -1216.75 322.08
## poly(Olaparib, 2)1:siRNAsi53BP1 -944.12 655.78
## poly(Olaparib, 2)2:siRNAsi53BP1 302.40 655.78
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1 1233.64 655.78
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1 1565.84 655.78
## poly(Olaparib, 2)1:siRNAsiBRCA1 199.10 655.78
## poly(Olaparib, 2)2:siRNAsiBRCA1 2351.59 655.78
## poly(Olaparib, 2)1:genotypeALC1KO -2177.12 655.78
## poly(Olaparib, 2)2:genotypeALC1KO 3444.07 655.78
## siRNAsi53BP1:genotypeALC1KO -182.19 455.49
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 28.87 455.49
## siRNAsiBRCA1:genotypeALC1KO 519.06 455.49
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO 2942.95 927.42
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO -1295.71 927.42
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO 1730.08 927.42
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -2295.16 927.42
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO 4018.95 927.42
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO -3685.15 927.42
## df t value
## (Intercept) 24.00 9.338
## poly(Olaparib, 2)1 80.00 -8.762
## poly(Olaparib, 2)2 80.00 -3.957
## siRNAsi53BP1 24.00 -0.123
## siRNAsi53BP1+siBRCA1 24.00 -1.568
## siRNAsiBRCA1 24.00 -3.681
## genotypeALC1KO 24.00 -3.778
## poly(Olaparib, 2)1:siRNAsi53BP1 80.00 -1.440
## poly(Olaparib, 2)2:siRNAsi53BP1 80.00 0.461
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1 80.00 1.881
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1 80.00 2.388
## poly(Olaparib, 2)1:siRNAsiBRCA1 80.00 0.304
## poly(Olaparib, 2)2:siRNAsiBRCA1 80.00 3.586
## poly(Olaparib, 2)1:genotypeALC1KO 80.00 -3.320
## poly(Olaparib, 2)2:genotypeALC1KO 80.00 5.252
## siRNAsi53BP1:genotypeALC1KO 24.00 -0.400
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 24.00 0.063
## siRNAsiBRCA1:genotypeALC1KO 24.00 1.140
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO 80.00 3.173
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO 80.00 -1.397
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO 80.00 1.865
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO 80.00 -2.475
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO 80.00 4.333
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO 80.00 -3.974
## Pr(>|t|)
## (Intercept) 1.84e-09 ***
## poly(Olaparib, 2)1 2.58e-13 ***
## poly(Olaparib, 2)2 0.000163 ***
## siRNAsi53BP1 0.902805
## siRNAsi53BP1+siBRCA1 0.130079
## siRNAsiBRCA1 0.001174 **
## genotypeALC1KO 0.000922 ***
## poly(Olaparib, 2)1:siRNAsi53BP1 0.153859
## poly(Olaparib, 2)2:siRNAsi53BP1 0.645960
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1 0.063586 .
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1 0.019310 *
## poly(Olaparib, 2)1:siRNAsiBRCA1 0.762222
## poly(Olaparib, 2)2:siRNAsiBRCA1 0.000576 ***
## poly(Olaparib, 2)1:genotypeALC1KO 0.001358 **
## poly(Olaparib, 2)2:genotypeALC1KO 1.21e-06 ***
## siRNAsi53BP1:genotypeALC1KO 0.692708
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.949978
## siRNAsiBRCA1:genotypeALC1KO 0.265711
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO 0.002139 **
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO 0.166242
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.065780 .
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.015446 *
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO 4.23e-05 ***
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO 0.000154 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
cat("AIC: ", AIC(fit8))
## AIC: 1479.072
simres <- simulateResiduals(fittedModel = fit8)
plot(simres)

Cubic formula
fit9 <- lm(Counts ~ Experiment + poly(Olaparib,3)*siRNA*genotype, data = dataset)
print(summary(fit9))
##
## Call:
## lm(formula = Counts ~ Experiment + poly(Olaparib, 3) * siRNA *
## genotype, data = dataset)
##
## Residuals:
## Min 1Q Median 3Q Max
## -682.5 -229.8 16.2 210.0 844.8
##
## Coefficients:
## Estimate Std. Error
## (Intercept) 1967.17 108.46
## Experimentexp2 445.94 92.49
## Experimentexp3 389.25 92.49
## Experimentexp4 -197.37 92.49
## poly(Olaparib, 3)1 -4063.13 1046.45
## poly(Olaparib, 3)2 -1834.91 1046.45
## poly(Olaparib, 3)3 -658.33 1046.45
## siRNAsi53BP1 -39.75 130.81
## siRNAsi53BP1+siBRCA1 -504.87 130.81
## siRNAsiBRCA1 -1185.69 130.81
## genotypeALC1KO -1216.75 130.81
## poly(Olaparib, 3)1:siRNAsi53BP1 -944.12 1479.91
## poly(Olaparib, 3)2:siRNAsi53BP1 302.40 1479.91
## poly(Olaparib, 3)3:siRNAsi53BP1 486.10 1479.91
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1 1233.64 1479.91
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1 1565.84 1479.91
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1 1284.68 1479.91
## poly(Olaparib, 3)1:siRNAsiBRCA1 199.10 1479.91
## poly(Olaparib, 3)2:siRNAsiBRCA1 2351.59 1479.91
## poly(Olaparib, 3)3:siRNAsiBRCA1 593.91 1479.91
## poly(Olaparib, 3)1:genotypeALC1KO -2177.12 1479.91
## poly(Olaparib, 3)2:genotypeALC1KO 3444.07 1479.91
## poly(Olaparib, 3)3:genotypeALC1KO 375.79 1479.91
## siRNAsi53BP1:genotypeALC1KO -182.19 184.99
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 28.87 184.99
## siRNAsiBRCA1:genotypeALC1KO 519.06 184.99
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO 2942.95 2092.91
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO -1295.71 2092.91
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO 77.89 2092.91
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO 1730.08 2092.91
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -2295.16 2092.91
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1183.92 2092.91
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO 4018.95 2092.91
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO -3685.15 2092.91
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO -196.83 2092.91
## t value Pr(>|t|)
## (Intercept) 18.137 < 2e-16 ***
## Experimentexp2 4.821 5.55e-06 ***
## Experimentexp3 4.208 5.93e-05 ***
## Experimentexp4 -2.134 0.035481 *
## poly(Olaparib, 3)1 -3.883 0.000193 ***
## poly(Olaparib, 3)2 -1.753 0.082819 .
## poly(Olaparib, 3)3 -0.629 0.530825
## siRNAsi53BP1 -0.304 0.761896
## siRNAsi53BP1+siBRCA1 -3.860 0.000209 ***
## siRNAsiBRCA1 -9.064 1.95e-14 ***
## genotypeALC1KO -9.302 6.14e-15 ***
## poly(Olaparib, 3)1:siRNAsi53BP1 -0.638 0.525069
## poly(Olaparib, 3)2:siRNAsi53BP1 0.204 0.838538
## poly(Olaparib, 3)3:siRNAsi53BP1 0.328 0.743300
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1 0.834 0.406646
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1 1.058 0.292766
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1 0.868 0.387587
## poly(Olaparib, 3)1:siRNAsiBRCA1 0.135 0.893273
## poly(Olaparib, 3)2:siRNAsiBRCA1 1.589 0.115452
## poly(Olaparib, 3)3:siRNAsiBRCA1 0.401 0.689108
## poly(Olaparib, 3)1:genotypeALC1KO -1.471 0.144636
## poly(Olaparib, 3)2:genotypeALC1KO 2.327 0.022124 *
## poly(Olaparib, 3)3:genotypeALC1KO 0.254 0.800114
## siRNAsi53BP1:genotypeALC1KO -0.985 0.327250
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.156 0.876300
## siRNAsiBRCA1:genotypeALC1KO 2.806 0.006111 **
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO 1.406 0.163011
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO -0.619 0.537367
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO 0.037 0.970393
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.827 0.410557
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1.097 0.275632
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.566 0.572973
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO 1.920 0.057888 .
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO -1.761 0.081563 .
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO -0.094 0.925276
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 370 on 93 degrees of freedom
## Multiple R-squared: 0.8721, Adjusted R-squared: 0.8254
## F-statistic: 18.66 on 34 and 93 DF, p-value: < 2.2e-16
cat("AIC: ", AIC(fit9))
## AIC: 1908.202
simres <- simulateResiduals(fittedModel = fit9)
plot(simres)

fit10 <- lm(NormCounts ~ poly(Olaparib,3)*siRNA*genotype, data = dataset)
print(summary(fit10))
##
## Call:
## lm(formula = NormCounts ~ poly(Olaparib, 3) * siRNA * genotype,
## data = dataset)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.48516 -0.08021 0.00374 0.08583 0.52791
##
## Coefficients:
## Estimate Std. Error
## (Intercept) 1.000e+00 4.223e-02
## poly(Olaparib, 3)1 -1.973e+00 4.778e-01
## poly(Olaparib, 3)2 -8.808e-01 4.778e-01
## poly(Olaparib, 3)3 -3.028e-01 4.778e-01
## siRNAsi53BP1 8.493e-17 5.973e-02
## siRNAsi53BP1+siBRCA1 3.307e-16 5.973e-02
## siRNAsiBRCA1 -6.790e-17 5.973e-02
## genotypeALC1KO -5.075e-16 5.973e-02
## poly(Olaparib, 3)1:siRNAsi53BP1 -5.603e-01 6.757e-01
## poly(Olaparib, 3)2:siRNAsi53BP1 1.255e-01 6.757e-01
## poly(Olaparib, 3)3:siRNAsi53BP1 2.073e-01 6.757e-01
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1 -1.515e-01 6.757e-01
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1 8.736e-01 6.757e-01
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1 5.385e-01 6.757e-01
## poly(Olaparib, 3)1:siRNAsiBRCA1 -2.295e+00 6.757e-01
## poly(Olaparib, 3)2:siRNAsiBRCA1 1.021e+00 6.757e-01
## poly(Olaparib, 3)3:siRNAsiBRCA1 3.140e-01 6.757e-01
## poly(Olaparib, 3)1:genotypeALC1KO -5.126e+00 6.757e-01
## poly(Olaparib, 3)2:genotypeALC1KO 2.709e+00 6.757e-01
## poly(Olaparib, 3)3:genotypeALC1KO -1.721e-01 6.757e-01
## siRNAsi53BP1:genotypeALC1KO -3.885e-17 8.447e-02
## siRNAsi53BP1+siBRCA1:genotypeALC1KO -4.261e-16 8.447e-02
## siRNAsiBRCA1:genotypeALC1KO -1.683e-16 8.447e-02
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO 1.163e+00 9.557e-01
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO -1.002e+00 9.557e-01
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO 5.200e-01 9.557e-01
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1.028e+00 9.557e-01
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1.787e-01 9.557e-01
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO -5.458e-01 9.557e-01
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO 1.182e+00 9.557e-01
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO -1.788e+00 9.557e-01
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO 6.968e-01 9.557e-01
## t value Pr(>|t|)
## (Intercept) 23.677 < 2e-16 ***
## poly(Olaparib, 3)1 -4.128 7.80e-05 ***
## poly(Olaparib, 3)2 -1.843 0.068359 .
## poly(Olaparib, 3)3 -0.634 0.527770
## siRNAsi53BP1 0.000 1.000000
## siRNAsi53BP1+siBRCA1 0.000 1.000000
## siRNAsiBRCA1 0.000 1.000000
## genotypeALC1KO 0.000 1.000000
## poly(Olaparib, 3)1:siRNAsi53BP1 -0.829 0.409047
## poly(Olaparib, 3)2:siRNAsi53BP1 0.186 0.853045
## poly(Olaparib, 3)3:siRNAsi53BP1 0.307 0.759698
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1 -0.224 0.823029
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1 1.293 0.199180
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1 0.797 0.427501
## poly(Olaparib, 3)1:siRNAsiBRCA1 -3.396 0.000995 ***
## poly(Olaparib, 3)2:siRNAsiBRCA1 1.511 0.134098
## poly(Olaparib, 3)3:siRNAsiBRCA1 0.465 0.643245
## poly(Olaparib, 3)1:genotypeALC1KO -7.585 2.12e-11 ***
## poly(Olaparib, 3)2:genotypeALC1KO 4.008 0.000121 ***
## poly(Olaparib, 3)3:genotypeALC1KO -0.255 0.799459
## siRNAsi53BP1:genotypeALC1KO 0.000 1.000000
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.000 1.000000
## siRNAsiBRCA1:genotypeALC1KO 0.000 1.000000
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO 1.217 0.226438
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO -1.048 0.297146
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO 0.544 0.587587
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1.076 0.284814
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.187 0.852038
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.571 0.569225
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO 1.237 0.219241
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO -1.871 0.064330 .
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO 0.729 0.467676
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.1689 on 96 degrees of freedom
## Multiple R-squared: 0.9263, Adjusted R-squared: 0.9025
## F-statistic: 38.94 on 31 and 96 DF, p-value: < 2.2e-16
cat("AIC: ", AIC(fit10))
## AIC: -62.8016
simres <- simulateResiduals(fittedModel = fit10)
plot(simres)

fit11 <- lm(NormCounts2 ~ poly(Olaparib,3)*siRNA*genotype, data = dataset)
print(summary(fit11))
##
## Call:
## lm(formula = NormCounts2 ~ poly(Olaparib, 3) * siRNA * genotype,
## data = dataset)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.228704 -0.042322 0.002445 0.054386 0.232250
##
## Coefficients:
## Estimate Std. Error
## (Intercept) 0.841093 0.023068
## poly(Olaparib, 3)1 -1.659109 0.260990
## poly(Olaparib, 3)2 -0.740846 0.260990
## poly(Olaparib, 3)3 -0.254690 0.260990
## siRNAsi53BP1 -0.050843 0.032624
## siRNAsi53BP1+siBRCA1 -0.050571 0.032624
## siRNAsiBRCA1 -0.198613 0.032624
## genotypeALC1KO -0.357112 0.032624
## poly(Olaparib, 3)1:siRNAsi53BP1 -0.342512 0.369096
## poly(Olaparib, 3)2:siRNAsi53BP1 0.143967 0.369096
## poly(Olaparib, 3)3:siRNAsi53BP1 0.179203 0.369096
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1 -0.020047 0.369096
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1 0.735155 0.369096
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1 0.440989 0.369096
## poly(Olaparib, 3)1:siRNAsiBRCA1 -1.082742 0.369096
## poly(Olaparib, 3)2:siRNAsiBRCA1 0.830908 0.369096
## poly(Olaparib, 3)3:siRNAsiBRCA1 0.261866 0.369096
## poly(Olaparib, 3)1:genotypeALC1KO -1.776242 0.369096
## poly(Olaparib, 3)2:genotypeALC1KO 1.625433 0.369096
## poly(Olaparib, 3)3:genotypeALC1KO 0.024820 0.369096
## siRNAsi53BP1:genotypeALC1KO 0.093085 0.046137
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.006535 0.046137
## siRNAsiBRCA1:genotypeALC1KO 0.186036 0.046137
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO 0.360026 0.521980
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO -0.527875 0.521980
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO 0.183467 0.521980
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.186264 0.521980
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.509928 0.521980
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.423311 0.521980
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO 0.647226 0.521980
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO -1.215675 0.521980
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO 0.220606 0.521980
## t value Pr(>|t|)
## (Intercept) 36.461 < 2e-16 ***
## poly(Olaparib, 3)1 -6.357 6.92e-09 ***
## poly(Olaparib, 3)2 -2.839 0.005530 **
## poly(Olaparib, 3)3 -0.976 0.331586
## siRNAsi53BP1 -1.558 0.122415
## siRNAsi53BP1+siBRCA1 -1.550 0.124404
## siRNAsiBRCA1 -6.088 2.35e-08 ***
## genotypeALC1KO -10.946 < 2e-16 ***
## poly(Olaparib, 3)1:siRNAsi53BP1 -0.928 0.355747
## poly(Olaparib, 3)2:siRNAsi53BP1 0.390 0.697361
## poly(Olaparib, 3)3:siRNAsi53BP1 0.486 0.628414
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1 -0.054 0.956799
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1 1.992 0.049237 *
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1 1.195 0.235116
## poly(Olaparib, 3)1:siRNAsiBRCA1 -2.933 0.004192 **
## poly(Olaparib, 3)2:siRNAsiBRCA1 2.251 0.026654 *
## poly(Olaparib, 3)3:siRNAsiBRCA1 0.709 0.479747
## poly(Olaparib, 3)1:genotypeALC1KO -4.812 5.54e-06 ***
## poly(Olaparib, 3)2:genotypeALC1KO 4.404 2.76e-05 ***
## poly(Olaparib, 3)3:genotypeALC1KO 0.067 0.946526
## siRNAsi53BP1:genotypeALC1KO 2.018 0.046427 *
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.142 0.887657
## siRNAsiBRCA1:genotypeALC1KO 4.032 0.000111 ***
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO 0.690 0.492028
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO -1.011 0.314418
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO 0.351 0.725996
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.357 0.721994
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.977 0.331069
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.811 0.419389
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO 1.240 0.218019
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO -2.329 0.021958 *
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO 0.423 0.673509
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.09227 on 96 degrees of freedom
## Multiple R-squared: 0.9367, Adjusted R-squared: 0.9162
## F-statistic: 45.82 on 31 and 96 DF, p-value: < 2.2e-16
cat("AIC: ", AIC(fit11))
## AIC: -217.6213
simres <- simulateResiduals(fittedModel = fit11)
plot(simres)

fit12 <- lmer(Counts ~ poly(Olaparib,3)*siRNA*genotype + (1|UID), data = dataset)
print(summary(fit12))
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Counts ~ poly(Olaparib, 3) * siRNA * genotype + (1 | UID)
## Data: dataset
##
## REML criterion at convergence: 1309.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.43519 -0.42342 0.02777 0.45257 2.33975
##
## Random effects:
## Groups Name Variance Std.Dev.
## UID (Intercept) 200467 447.7
## Residual 28016 167.4
## Number of obs: 128, groups: UID, 32
##
## Fixed effects:
## Estimate Std. Error
## (Intercept) 2126.62 227.74
## poly(Olaparib, 3)1 -4063.13 473.42
## poly(Olaparib, 3)2 -1834.91 473.42
## poly(Olaparib, 3)3 -658.33 473.42
## siRNAsi53BP1 -39.75 322.08
## siRNAsi53BP1+siBRCA1 -504.87 322.08
## siRNAsiBRCA1 -1185.69 322.08
## genotypeALC1KO -1216.75 322.08
## poly(Olaparib, 3)1:siRNAsi53BP1 -944.12 669.52
## poly(Olaparib, 3)2:siRNAsi53BP1 302.40 669.52
## poly(Olaparib, 3)3:siRNAsi53BP1 486.10 669.52
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1 1233.64 669.52
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1 1565.84 669.52
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1 1284.68 669.52
## poly(Olaparib, 3)1:siRNAsiBRCA1 199.10 669.52
## poly(Olaparib, 3)2:siRNAsiBRCA1 2351.59 669.52
## poly(Olaparib, 3)3:siRNAsiBRCA1 593.91 669.52
## poly(Olaparib, 3)1:genotypeALC1KO -2177.12 669.52
## poly(Olaparib, 3)2:genotypeALC1KO 3444.07 669.52
## poly(Olaparib, 3)3:genotypeALC1KO 375.79 669.52
## siRNAsi53BP1:genotypeALC1KO -182.19 455.49
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 28.87 455.49
## siRNAsiBRCA1:genotypeALC1KO 519.06 455.49
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO 2942.95 946.85
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO -1295.71 946.85
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO 77.89 946.85
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO 1730.08 946.85
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -2295.16 946.85
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1183.92 946.85
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO 4018.95 946.85
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO -3685.15 946.85
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO -196.83 946.85
## df t value
## (Intercept) 24.00 9.338
## poly(Olaparib, 3)1 72.00 -8.582
## poly(Olaparib, 3)2 72.00 -3.876
## poly(Olaparib, 3)3 72.00 -1.391
## siRNAsi53BP1 24.00 -0.123
## siRNAsi53BP1+siBRCA1 24.00 -1.568
## siRNAsiBRCA1 24.00 -3.681
## genotypeALC1KO 24.00 -3.778
## poly(Olaparib, 3)1:siRNAsi53BP1 72.00 -1.410
## poly(Olaparib, 3)2:siRNAsi53BP1 72.00 0.452
## poly(Olaparib, 3)3:siRNAsi53BP1 72.00 0.726
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1 72.00 1.843
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1 72.00 2.339
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1 72.00 1.919
## poly(Olaparib, 3)1:siRNAsiBRCA1 72.00 0.297
## poly(Olaparib, 3)2:siRNAsiBRCA1 72.00 3.512
## poly(Olaparib, 3)3:siRNAsiBRCA1 72.00 0.887
## poly(Olaparib, 3)1:genotypeALC1KO 72.00 -3.252
## poly(Olaparib, 3)2:genotypeALC1KO 72.00 5.144
## poly(Olaparib, 3)3:genotypeALC1KO 72.00 0.561
## siRNAsi53BP1:genotypeALC1KO 24.00 -0.400
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 24.00 0.063
## siRNAsiBRCA1:genotypeALC1KO 24.00 1.140
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO 72.00 3.108
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO 72.00 -1.368
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO 72.00 0.082
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO 72.00 1.827
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO 72.00 -2.424
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO 72.00 -1.250
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO 72.00 4.245
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO 72.00 -3.892
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO 72.00 -0.208
## Pr(>|t|)
## (Intercept) 1.84e-09 ***
## poly(Olaparib, 3)1 1.25e-12 ***
## poly(Olaparib, 3)2 0.000232 ***
## poly(Olaparib, 3)3 0.168641
## siRNAsi53BP1 0.902805
## siRNAsi53BP1+siBRCA1 0.130079
## siRNAsiBRCA1 0.001174 **
## genotypeALC1KO 0.000922 ***
## poly(Olaparib, 3)1:siRNAsi53BP1 0.162804
## poly(Olaparib, 3)2:siRNAsi53BP1 0.652870
## poly(Olaparib, 3)3:siRNAsi53BP1 0.470172
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1 0.069508 .
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1 0.022128 *
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1 0.058975 .
## poly(Olaparib, 3)1:siRNAsiBRCA1 0.767041
## poly(Olaparib, 3)2:siRNAsiBRCA1 0.000771 ***
## poly(Olaparib, 3)3:siRNAsiBRCA1 0.377997
## poly(Olaparib, 3)1:genotypeALC1KO 0.001747 **
## poly(Olaparib, 3)2:genotypeALC1KO 2.23e-06 ***
## poly(Olaparib, 3)3:genotypeALC1KO 0.576353
## siRNAsi53BP1:genotypeALC1KO 0.692708
## siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.949978
## siRNAsiBRCA1:genotypeALC1KO 0.265711
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO 0.002695 **
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO 0.175428
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO 0.934667
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.071813 .
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.017864 *
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.215209
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO 6.43e-05 ***
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO 0.000220 ***
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO 0.835913
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
cat("AIC: ", AIC(fit12))
## AIC: 1377.126
simres <- simulateResiduals(fittedModel = fit12)
plot(simres)

Final Result
fit <- fit7
output <- coef(summary(fit))
output <- output[grep("Olaparib", rownames(output)),]
rownames(output) <- gsub("poly\\(|, [1-3]\\)","", rownames(output) )
rownames(output) <- gsub("genotype", paste0(" ",levels(dataset$genotype)[1], " vs. "), rownames(output))
rownames(output)[!(grepl("vs", rownames(output)))] <- paste(rownames(output)[!(grepl("vs", rownames(output)))], levels(dataset$genotype)[1], sep = " in " )
rownames(output) <- gsub("siRNA", paste0(" ",levels(dataset$siRNA)[1], " vs. "), rownames(output))
rownames(output)[!(grepl("vs.*vs|in", rownames(output)))] <- paste(rownames(output)[!(grepl("vs.*vs|in", rownames(output)))], levels(dataset$siRNA)[1], sep = " in " )
rownames(output)[!(grepl("vs", rownames(output)))] <- paste(rownames(output)[!(grepl("vs", rownames(output)))], levels(dataset$siRNA)[1], sep = " " )
# suggested result table
kable(output, row.names = T)
| Olaparib1 in WT siCtrl |
-1.6591091 |
0.2561505 |
-6.4770871 |
0.0000000 |
| Olaparib2 in WT siCtrl |
-0.7408465 |
0.2561505 |
-2.8922312 |
0.0046590 |
| Olaparib1: siCtrl vs. si53BP1 in WT |
-0.3425124 |
0.3622515 |
-0.9455099 |
0.3465902 |
| Olaparib2: siCtrl vs. si53BP1 in WT |
0.1439674 |
0.3622515 |
0.3974238 |
0.6918695 |
| Olaparib1: siCtrl vs. si53BP1+siBRCA1 in WT |
-0.0200466 |
0.3622515 |
-0.0553389 |
0.9559746 |
| Olaparib2: siCtrl vs. si53BP1+siBRCA1 in WT |
0.7351549 |
0.3622515 |
2.0294045 |
0.0449712 |
| Olaparib1: siCtrl vs. siBRCA1 in WT |
-1.0827417 |
0.3622515 |
-2.9889225 |
0.0034938 |
| Olaparib2: siCtrl vs. siBRCA1 in WT |
0.8309079 |
0.3622515 |
2.2937320 |
0.0238166 |
| Olaparib1: WT vs. ALC1KO in siCtrl |
-1.7762418 |
0.3622515 |
-4.9033385 |
0.0000035 |
| Olaparib2: WT vs. ALC1KO in siCtrl |
1.6254326 |
0.3622515 |
4.4870277 |
0.0000187 |
| Olaparib1: siCtrl vs. si53BP1: WT vs. ALC1KO |
0.3600258 |
0.5123010 |
0.7027623 |
0.4837740 |
| Olaparib2: siCtrl vs. si53BP1: WT vs. ALC1KO |
-0.5278751 |
0.5123010 |
-1.0304002 |
0.3052125 |
| Olaparib1: siCtrl vs. si53BP1+siBRCA1: WT vs. ALC1KO |
-0.1862640 |
0.5123010 |
-0.3635831 |
0.7169074 |
| Olaparib2: siCtrl vs. si53BP1+siBRCA1: WT vs. ALC1KO |
-0.5099282 |
0.5123010 |
-0.9953684 |
0.3218674 |
| Olaparib1: siCtrl vs. siBRCA1: WT vs. ALC1KO |
0.6472261 |
0.5123010 |
1.2633708 |
0.2092808 |
| Olaparib2: siCtrl vs. siBRCA1: WT vs. ALC1KO |
-1.2156753 |
0.5123010 |
-2.3729707 |
0.0194828 |
write.table(output, file = "FigureS5A_Stats_Ref_WT.txt", quote = F, sep = "\t", row.names = T, col.names = NA)
# re-fit with ALC1KO reference
dataset$genotype <- relevel(dataset$genotype, ref = "ALC1KO")
fit <- lm(NormCounts2 ~ poly(Olaparib,2)*siRNA*genotype, data = dataset)
output <- coef(summary(fit))
output <- output[grep("Olaparib", rownames(output)),]
rownames(output) <- gsub("poly\\(|, [1-3]\\)","", rownames(output) )
rownames(output) <- gsub("genotype", paste0(" ",levels(dataset$genotype)[1], " vs. "), rownames(output))
rownames(output)[!(grepl("vs", rownames(output)))] <- paste(rownames(output)[!(grepl("vs", rownames(output)))], levels(dataset$genotype)[1], sep = " in " )
rownames(output) <- gsub("siRNA", paste0(" ",levels(dataset$siRNA)[1], " vs. "), rownames(output))
rownames(output)[!(grepl("vs.*vs|in", rownames(output)))] <- paste(rownames(output)[!(grepl("vs.*vs|in", rownames(output)))], levels(dataset$siRNA)[1], sep = " in " )
rownames(output)[!(grepl("vs", rownames(output)))] <- paste(rownames(output)[!(grepl("vs", rownames(output)))], levels(dataset$siRNA)[1], sep = " " )
# suggested result table
kable(output, row.names = T)
| Olaparib1 in ALC1KO siCtrl |
-3.4353509 |
0.2561505 |
-13.4114549 |
0.0000000 |
| Olaparib2 in ALC1KO siCtrl |
0.8845861 |
0.2561505 |
3.4533843 |
0.0008020 |
| Olaparib1: siCtrl vs. si53BP1 in ALC1KO |
0.0175134 |
0.3622515 |
0.0483460 |
0.9615332 |
| Olaparib2: siCtrl vs. si53BP1 in ALC1KO |
-0.3839077 |
0.3622515 |
-1.0597822 |
0.2916988 |
| Olaparib1: siCtrl vs. si53BP1+siBRCA1 in ALC1KO |
-0.2063106 |
0.3622515 |
-0.5695231 |
0.5702293 |
| Olaparib2: siCtrl vs. si53BP1+siBRCA1 in ALC1KO |
0.2252266 |
0.3622515 |
0.6217411 |
0.5354727 |
| Olaparib1: siCtrl vs. siBRCA1 in ALC1KO |
-0.4355156 |
0.3622515 |
-1.2022465 |
0.2319983 |
| Olaparib2: siCtrl vs. siBRCA1 in ALC1KO |
-0.3847674 |
0.3622515 |
-1.0621553 |
0.2906254 |
| Olaparib1: ALC1KO vs. WT in siCtrl |
1.7762418 |
0.3622515 |
4.9033385 |
0.0000035 |
| Olaparib2: ALC1KO vs. WT in siCtrl |
-1.6254326 |
0.3622515 |
-4.4870277 |
0.0000187 |
| Olaparib1: siCtrl vs. si53BP1: ALC1KO vs. WT |
-0.3600258 |
0.5123010 |
-0.7027623 |
0.4837740 |
| Olaparib2: siCtrl vs. si53BP1: ALC1KO vs. WT |
0.5278751 |
0.5123010 |
1.0304002 |
0.3052125 |
| Olaparib1: siCtrl vs. si53BP1+siBRCA1: ALC1KO vs. WT |
0.1862640 |
0.5123010 |
0.3635831 |
0.7169074 |
| Olaparib2: siCtrl vs. si53BP1+siBRCA1: ALC1KO vs. WT |
0.5099282 |
0.5123010 |
0.9953684 |
0.3218674 |
| Olaparib1: siCtrl vs. siBRCA1: ALC1KO vs. WT |
-0.6472261 |
0.5123010 |
-1.2633708 |
0.2092808 |
| Olaparib2: siCtrl vs. siBRCA1: ALC1KO vs. WT |
1.2156753 |
0.5123010 |
2.3729707 |
0.0194828 |
write.table(output, file = "FigureS5A_Stats_Ref_ALC1.txt", quote = F, sep = "\t", row.names = T, col.names = NA)